Dev beagle clean

[spydr073]

This branch allows for users to choose to use BEAGLE as a backend for likelihood calculations. There are 2 additional dependencies that must be installed to compile with BEAGLE support: BEAGLE-LIB and Eigen3.

Implemented:

• Selecting and using BEAGLE enabled devices (cpu, sse, avx, gpu, opencl, cuda)
• Settings for BEAGLE scaling, float/double, threading
• Likelihood calculations for single matrix substitution models (JC, HKY, F81, GTR, etc.)
• Among Site Rate Variation (ASRV)
• Invariable sites (+I)
• Choice of using eigensystems or per-node transition matrices for likelihood calculations (eigen way is prefered)

Partially Implemented:

• Currently there is a problem using ASRV and the per-node transition matrices backend (ASRV currently just works with the eigen backend)
• Mixture Models are partially implemented. I was unable to figure out how to set the category weights for the mixtures properly in BEAGLE.

Not Implemented:

• Partitioned analyses
• Using BEAGLE with MPI

To compile:

• ./build.sh -beagle true -eigen true

Commands and options to use in Rev scripts to use BEAGLE:

beagleInfo()
setOption("useBeagle", <boolean>)
setOption("beagleDevice", <natural>)
setOption("beagleResource", <beagle_resource>)
setOption("beagleDoublePrecision", <boolean>)
setOption("beagleMaxCPUThreads", <natural>)
setOption("beagleScalingMode", <scaling_mode>)
setOption("beagleDynamicScalingFrequency", <natural>)

beagle_resource options:

cpu
cpu_sse
cpu_avx
gpu_opencl
gpu_cuda

scaling_mode options:

manual
auto
always
dynamic

When using dynamic scaling, users may also want to set the beagleDynamicScalingFrequency.
The default scaling frequency is 100.

[bredelings]

Hi Killian,

1. can you rebase this onto origin/development? There are a number of merge conflict you would need to solve. If you have questions about how to do this, you can message me on slack.

2. if the BEAGLE code can't handle ASRV, what do you propose for the running tests? Ideally we should be testing the eigen and beagle configurations.

-BenRI

[bredelings]

I think this is the wrong branch. It looks like the right branch is dev_beagle. Is that right?